Isolation and chromosomal assignment of canine genomic BAC clones representing 25 cancer-related genes

An extensive number of genes have been implicated in the initiation and progression of human cancers, aiding our understanding of the genetic aetiology of this highly heterogeneous disease. In order to facilitate extrapolation of such information between species, we have isolated and physically mapped the canine orthologues of 25 well-characterised human cancer-related genes. The identity of PCR products representing each canine gene marker was first confirmed by DNA sequencing analysis. Each product was then radiolabelled and used to screen a genomic BAC library for the domestic dog. The chromosomal location of each positive clone in the canine karyotype was determined by fluorescence in situ hybridisation (FISH) onto canine metaphase preparations. Of the 25 genes, the FISH localisation of 21 correlated fully with that expected on the basis of known regions of conserved synteny between the human and canine genomes. Three correlated less closely, and the chromosomal location of the remaining marker showed no apparent correlation with current comparative mapping data. In addition to generating useful comparative mapping information, this panel of markers will act as a valuable resource for detailed study of candidate genes likely to be involved in tumourigenesis, and also forms the basis of a canine cancer-gene genomic microarray currently being developed for the study of unbalanced genomic aberrations in canine tumours.     

Expression and interaction analysis of Arabidopsis Skp1-related genes

Specific protein degradation has been observed in several aspects of development and differentiation in many organisms. One example of such proteolysis is regulated by protein polyubiquitination that is promoted by the SCF complex consisting of Skp1, cullin, and an F-box protein. We examined the activities of the Arabidopsis Skp1-related proteins (ASKs). Among 19 annotated ASK genes, we isolated 16 of the corresponding cDNAs (ASK1, 2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19), and examined their gene products for interactions with 24 representatives of F-box proteins carrying various classes of the C-terminal domains using the yeast two-hybrid system. As a result, we found diverse binding specificities: ASK1, ASK2, ASK11 and ASK12 interacted well with COI1, FKF1, UFO-like protein, LRR-containing F-box proteins, and other F-box proteins with unknown C-terminal motifs. We also observed specific interaction between F-box proteins and ASK3, ASK9, ASK13, ASK14, ASK16 and ASK18. In contrast, we detected no interaction between any of the 12 ASK proteins and F-box proteins containing CRFA, CRFB or CRFC domains. Both histochemical and RT-PCR analysis of eight ASK genes expression revealed unique expression patterns for the respective genes.     

Comparative analysis of the structure and chromosomal assignment ofCD1: an evidence for different evolutionary histories between classic CD1 and CD1D class genes

The non-MHC-encoded CD1 family has recently emerged as a novel antigen-presenting system that is distinct from MHC class I and class II molecules. In the present study, we determined the genomic structure of that rat CD1, and compared with those of other previously reported CD1 genes. Rat CD1 was extremely similar to mouse CD1 genes, especially to CD1D1. It is of interest that a tyrosine-based motif for endosomal localization, identified in the human CD1b cytoplasmic tail, was conserved in all CD1 molecules except for CD1a, that was encoded by a single short exon. Comparison of the overall exon-intron organization of CD1 genes revealed that the length of the introns was also characteristic to each of the two classes of CD1 genes; classic (CD1A, CD1B, CD1C and CD1E), and CD1D, which have been categorized by comparison of coding regions. These findings support a hypothesis that the two classes have different evolutionary histories. In contrast to the absence of the classic CD1 genes in rats and mice, the entire region of nonpolymorphic CD1D gene has been conserved through mammalian evolution. Furthermore, we determined chromosomal localization of rat CD1 gene using the fluorescence in situ hybridization method with several probes derived from genomic rat CD1 clones. Similar to human and mouse CD1, rat CD1 mapped outside the MHC loci despite the structural and functional resemblance to MHC. Conserved syntheny of chromosomal segments of RNO2 and MMU3 is implied.     

Molecular cloning and analysis of Staphylococcus aureus chromosomal aminoglycoside resistance genes

Most of the aminoglycoside resistant Staphylococcus aureus strains isolated in France are resistant to all the antibiotics belonging to this family. Two aminoglycoside-modifying enzymes were detected in the wild-type strains studied: an APH3'III and an AAC6'-APH2". These strains also carry two types of streptomycin resistance: high-level resistance due to chromosomal mutation(s) affecting ribosome affinity and low-level resistance, the mechanism of which was not characterized. All the aminoglycoside resistance genes were located on the chromosome. DNA fragments of 1.5 and 1.95 kb carrying the aphA and aacA genes, respectively, were isolated, by cloning, from the cellular DNA of a clinical isolate. When these genes were introduced into Escherichia coli and Bacillus subtilis strains, the enzymes synthesized were indistinguishable from those produced by the S. aureus strains. When the cellular DNAs of wild-type and resistant strains were hybridized with the cloned fragments, sequences homologous to the fragment carrying the aphA gene were found to be located at the same chromosomal site, while those hybridizing with the fragment carrying the aacA gene were at different chromosomal sites.     

Genomic cloning and chromosomal assignment of rat regucalcin gene

The gene for a Ca²⁺-binding protein regucalcin was cloned from a rat genomic library which was constructed in FIX II by screening with radiolabeled probe (complementary DNA of rat liver regucalcin). Positive clone had 19.9 kb insert of size and contained four exons of the gene coding for a rat regucalcin. These exons included the partial coding sequence (61.2% of open reading frame) and the entire 3-untranslated region of the gene. The nucleotide sequence of exons completely agreed with that of a rat regucalcin cDNA clone. The sequence analysis of the clone showed that the identifier sequence and two simple repeated sequences exist in the intron of the gene. Moreover, chromosomal location of the rat regucalcin gene was determined by direct R-banding fluorescencein situ hybridization (FISH) method with the 19.9 kb clone containing four exons. The regucalcin gene was localized on rat chromosome Xq11.1–12 proximal end.The nucleotide sequence data reported in this paper will appear in the DDBJ, EMBL and GenBank Nucleotide Sequence Databases with the following accession number D31662     

Proteome-wide Dysregulation by PRA1 Depletion Delineates a Role of PRA1 in Lipid Transport and Cell Migration

We have previously identified prenylated Rab acceptor 1 (PRA1) as a novel cellular interacting partner for Epstein-Barr virus-encoded oncoprotein, latent membrane protein 1 (LMP1). The intracellular trafficking and full signaling of LMP1 requires its interaction with PRA1. To further explore the role of PRA1 in Epstein-Barr virus-associated nasopharyngeal carcinoma (NPC) cells, we generated several PRA1-knockdown cell clones, which exhibited altered cell morphology and increased cell motility. We identified proteins differentially expressed in the knockdown clones by means of isobaric mass tags labeling coupled with multidimensional liquid chromatography-mass spectrometry. We validated a panel of proteins, which showed consistent up-regulation in PRA1-knockdown clones and participated in regulating lipid homeostasis and cell migration. Immunofluorescence staining further revealed altered localization of these proteins and accumulation of intracellular cholesterol in PRA1-knockdown clones. These effects were phenocopied by treatment with a cholesterol transport inhibitor, U18666A. Moreover, overexpressed PRA1 was able to alleviate the dysregulation of these affected proteins either from PRA1 knockdown or U18666A treatment, implying a role for PRA1 in regulating the levels of these affected proteins in response to altered cholesterol homeostasis. We further demonstrated that LMP1 expression caused PRA1 sequestration in NPC cells, leading to a consequence reminiscent of PRA1 knockdown. Finally, the immunohistochemistry showed a physiological relevance of the PRA1-associated proteome-wide changes in NPC biopsy tissues. In sum, our findings delineated novel roles of PRA1 in lipid transport and cell migration, and provided additional insights into the molecular basis of NPC morphogenesis, namely a consequence of LMP1-PRA1 interaction.Prenylated Rab acceptor 1 (PRA1)¹, which is a transmembrane protein of 21 kDa, is ubiquitously expressed in human tissues and localizes at the Golgi apparatus, post-Golgi vesicles, endosomes, and the plasma membrane (1, 2). As revealed by its name, PRA1 interacts with numerous Rab GTPases (2, 3), the latter of which function in a wide variety of biological processes such as endocytosis and exocytosis and have emerging roles in diseases (4–6). The PRA1-Rab interactions may assist in the packaging of Rabs into vesicles for transport to the destined compartments (2). Moreover, PRA1 also acts as a dual receptor for vesicle-associated membrane protein 2 (VAMP2) and GDP dissociation inhibitor 1 (GDI1) (7, 8). As a GDI displacement factor, PRA1 is able to catalytically dissociate endosomal Rabs (Rab9 and Rab5) from GDI-bound complexes and thereby escorts the liberated Rabs onto membranes (9). Given this relative lack of Rab specificity, PRA1-mediated regulation of Rab proteins is probably restricted by the cellular localization of PRA1, i.e. PRA1 regulates the Rabs present in the organelles with which PRA1 associates.Although its precise physical role remains to be better elucidated, PRA1 seems to function in the regulation of docking and fusion of transport vesicles both in the Golgi apparatus and at the plasma membrane, or alternately function as a sorting protein in the Golgi apparatus (10). PRA1 can form a complex with Rab3a and VAMP2, and the interaction of this complex can result in VAMP2 activation (7). Once activated, VAMP2 interacts with syntaxin, followed by the docking and fusion of transport vesicles with target membrane (11). Since syntaxin and VAMP2 are enriched in Golgi-derived lipid rafts (12), PRA1 is thought to associate with lipid rafts (13).As a platform for lipid-lipid and lipid-protein interactions, lipid rafts play critical roles in protein transport, sorting, targeting, signaling as well as membrane trafficking, and are essential for enveloped virus budding and assembly (14). In agreement with this notion, several viral proteins have been shown to interact with PRA1 to benefit the survival of viruses. For instance, the spike protein VP4 encoded by rotavirus and the envelope transmembrane protein gp41 encoded by retrovirus can interact with PRA1, and their interaction with PRA1 may in turn enhance the assembly of rotavirus and retrovirus particles, respectively (13, 15). In this regard, it is conceivable to speculate a role for PRA1 in promoting or stabilizing protein association with lipid rafts.In the previous study, we have identified PRA1 as a novel binding partner for the Epstein-Barr virus (EBV)-encoded oncoprotein, latent membrane protein 1 (LMP1) (16). EBV is closely associated with human diseases including nasopharyngeal carcinoma (NPC) (17), which is one of the common cancers in Taiwan and southern China, and LMP1 is shown to mainly contribute to these EBV-associated malignancies (18). By mimicking members of tumor necrosis factor receptor (TNFR) family, LMP1 can induce several signaling pathways in a constitutively-activated manner to exert its oncogenic potency (19–21). Importantly, the intracellular trafficking of LMP1 requires its interaction with PRA1, and this requirement is critical for full activation of LMP1-meditaed signaling (16). Accordingly, delineating the propensity of PRA would shed light on the nature of PRA1-LMP1 interaction and yield additional insights into the tumorigenesis of NPC.To further assess the role of PRA1 in NPC cells, in this study we generated several PRA1-knockdown NPC cell clones, which displayed altered cell morphology, and used these clones to analyze the effect of PRA1 on cell morphology and relevant biological processes. We discovered a panel of dysregulated proteins in PRA1-knockdown clones, which participate in lipid metabolism and transport and cell adhesion and migration, by using isobaric mass tags (iTRAQ) labeling approaches combined with multidimensional liquid chromatography-mass spectrometry (LC-MS/MS). To determine the physiological relevancy of our findings, we investigated the functional consequence of PRA1 sequestration in LMP1-expressing cells. We confirmed the phenotype of LMP1-expressing cells, namely intracellular cholesterol accumulation, elevated expression levels of those PRA1-affected proteins, and increased cell motility, consistent with the effect of PRA1 knockdown. We also validated the PRA1-associated dysregulation of selected proteins in NPC tissues using immunohistochemistry.Taken together, our findings revealed a PRA1-involved modulation in lipid homeostasis and cell migration, and implied an unexpected association of the LMP1-PRA1 interaction with NPC morphogenesis.     

Molecular cloning, characterization, and chromosomal assignment of porcine cationic amino acid transporter-1

We have cloned and characterized the gene encoding the porcine cationic amino acid transporter, member 1 (CAT-1) (HGMW-approved gene symbol SLC7A1) from porcine pulmonary artery endothelial cells. The porcine SLC7A1 encodes 629 deduced amino acid residues showing a higher degree of sequence similarity with the human counterpart (91.1%) than with the rat (87.3%) and mouse (87.6%) counterparts. Confocal microscopic examination of porcine CAT-1-GFP-expressing HEK293 cells revealed that porcine CAT-1 localizes on the plasma membrane. Amino acid uptake studies in Xenopus oocytes injected with cRNA encoding this protein demonstrated transport properties consistent with system y(+). Radiation hybrid mapping data indicate that the porcine SLC7A1 maps to the distal end of the short arm of pig chromosome 11 (SSC11). This map location is consistent with the known conservation of genome organization between human and pig and provides further confirmation that we have characterized the porcine orthologue of the human SLC7A1.     

Drosophila resistance genes to parasitoids: chromosomal location and linkage analysis

Insect hosts can survive infection by parasitoids using the encapsulation phenomenon. In Drosophila melanogaster the abilities to encapsulate the wasp species Leptopilina boulardi and Asobara tabida each involve one major gene. Both resistance genes have been precisely localized on the second chromosome, 35 centimorgans apart. This result clearly demonstrates the involvement of at least two separate genetic systems in Drosophila resistance to parasitoid wasps. The resistance genes to L. boulardi and A. tabida are not clustered as opposed to many plant resistance genes to pathogens cloned to date.     

Structural organization and chromosomal assignment of the gene encoding endothelin

Endothelin is a 21-amino acid vasoconstrictor synthesized and secreted by vascular endothelial cells. The human peptide is derived from a 212-amino acid precursor, preproendothelin. A nearly full length clone containing DNA complementary to human preproendothelin mRNA was isolated, and its nucleotide sequence was determined. Using this cDNA as a probe, the genomic organization of the human endothelin gene was determined and the promoter region delineated. The gene contains five exons and four intervening sequences. Nucleotide sequences encoding endothelin are contained within the second exon, and the third exon specifies a portion of preproendothelin that is homologous to endothelin. The second and third exons may represent descendants of a common progenitor exon. The 3'-untranslated portion of the gene contains a 250-base pair region that is highly conserved between human and porcine genomes and may have an important role in endothelin mRNA stability. On the basis of DNA isolated from human-mouse somatic hybrid cell lines, the endothelin gene was assigned to human chromosome 6.     

Creation and analysis of a bank of chromosomal genes of Streptococcus group A

The representative genomic library of chromosomal genes has been constructed for streptococcus group A serotype M48 strain 1/64 on the vector lambda L 47.1. Screening of the obtained genomic library by hybridization and immunological techniques revealed about 50 clones producing the streptococcal antigens (extracellular nonidentified products and non-type specific structural streptococcal proteins). Among the recombinant clones three were found to harbour the genetic determinants for M-protein. One the clones contains a determinant coding for epitopes crossreacting with antisera to M-proteins of other serotypes and a protective epitope. The presence of the latter was tested in an indirect bactericidal test.     

Structures and chromosomal localizations of two human genes encoding synaptobrevins 1 and 2

Synaptobrevins 1 and 2 are small integral membrane proteins specific for synaptic vesicles in neurons. Two cosmid clones containing the human genes encoding synaptobrevins 1 and 2 (gene symbols SYB1 and SYB2, respectively) were isolated and characterized. The coding regions of the synaptobrevin genes are highly homologous to each other and are interrupted at identical positions by introns of different size and sequence. Each gene is organized into five exons whose boundaries correspond to those of the protein domains. Exon I contains part of the initiator methionine codon whereas exon II encodes the variable and immunogenic amino-terminal domain of the synaptobrevins. The third exon comprises the highly conserved central domain of the synaptobrevins, exon IV encodes most of the transmembrane region, and exon V contains the last residues of the transmembrane region and the small intravesicular carboxyl terminus. Comparisons of the synaptobrevin sequences in five species from Drosophila with man indicate a selective conservation of sequences adjacent to the synaptic vesicle surface, suggesting a function at the membrane-cystosol interface. The chromosomal localizations of the human and mouse SYB1 and SYB2 genes were determined using hybrid cell lines. SYB1 was localized to the short arm of human chromosome 12 and to mouse chromosome 6 whereas SYB2 was found on the distal portion of the short arm of human chromosome 17 and on mouse chromosome 11. A PstI restriction fragment length polymorphism was identified at the SYB2 locus.